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comparison qiime2-2020.8/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_iqtree-ultrafast-bootstrap" name="qiime phylogeny iqtree-ultrafast-bootstrap"
3 version="2020.8">
4 <description>Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime phylogeny iqtree-ultrafast-bootstrap
10
11 --i-alignment=$ialignment
12
13 #if str($pseed):
14 --p-seed=$pseed
15 #end if
16 #if str($pncores) != 'None':
17 --p-n-cores=$pncores
18 #end if
19
20 #set $pncoresmax = '${GALAXY_SLOTS:-4}'
21
22 #if str($pncoresmax):
23 --p-n-cores-max=$pncoresmax
24 #end if
25
26 --p-n-runs=$pnruns
27
28 #if str($psubstitutionmodel) != 'None':
29 --p-substitution-model=$psubstitutionmodel
30 #end if
31
32 --p-bootstrap-replicates=$pbootstrapreplicates
33
34 #if str($pninitparstrees):
35 --p-n-init-pars-trees=$pninitparstrees
36 #end if
37 #if str($pntopinittrees):
38 --p-n-top-init-trees=$pntopinittrees
39 #end if
40 #if str($pnbestretaintrees):
41 --p-n-best-retain-trees=$pnbestretaintrees
42 #end if
43 #if str($pstopiter):
44 --p-stop-iter=$pstopiter
45 #end if
46 #if str($pperturbnnistrength):
47 --p-perturb-nni-strength=$pperturbnnistrength
48 #end if
49 #if str($psprradius):
50 --p-spr-radius=$psprradius
51 #end if
52 #if str($pnmaxufbootiter):
53 --p-n-max-ufboot-iter=$pnmaxufbootiter
54 #end if
55 #if str($pnufbootsteps):
56 --p-n-ufboot-steps=$pnufbootsteps
57 #end if
58 #if str($pmincorufboot):
59 --p-min-cor-ufboot=$pmincorufboot
60 #end if
61 #if str($pepbreakufboot):
62 --p-ep-break-ufboot=$pepbreakufboot
63 #end if
64 #if $pallnni:
65 --p-allnni
66 #end if
67
68 #if str($palrt):
69 --p-alrt=$palrt
70 #end if
71 #if $pabayes:
72 --p-abayes
73 #end if
74
75 #if str($plbp):
76 --p-lbp=$plbp
77 #end if
78 #if $pbnni:
79 --p-bnni
80 #end if
81
82 #if $psafe:
83 --p-safe
84 #end if
85
86 --o-tree=otree
87
88 #if str($examples) != 'None':
89 --examples=$examples
90 #end if
91
92 ;
93 cp otree.qza $otree
94
95 ]]></command>
96 <inputs>
97 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data" />
98 <param label="--p-seed: INTEGER Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="False" type="text" />
99 <param label="--p-n-cores: " name="pncores" optional="True" type="select">
100 <option selected="True" value="None">Selection is Optional</option>
101 <option value="Int % Range(1">Int % Range(1</option>
102 <option value="None">None</option>
103 </param>
104 <param label="--p-n-runs: INTEGER Number of indepedent runs. Multiple independent Range(1, None) runs (e.g. 10) can outperform a single run in terms of likelihood maximisation. [default: 1]" min="1" name="pnruns" optional="True" type="integer" value="1" />
105 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
106 <option selected="True" value="None">Selection is Optional</option>
107 <option value="JC">JC</option>
108 <option value="JC+I">JC+I</option>
109 <option value="JC+G">JC+G</option>
110 <option value="JC+I+G">JC+I+G</option>
111 <option value="JC+R2">JC+R2</option>
112 <option value="JC+R3">JC+R3</option>
113 <option value="JC+R4">JC+R4</option>
114 <option value="JC+R5">JC+R5</option>
115 <option value="JC+R6">JC+R6</option>
116 <option value="JC+R7">JC+R7</option>
117 <option value="JC+R8">JC+R8</option>
118 <option value="JC+R9">JC+R9</option>
119 <option value="JC+R10">JC+R10</option>
120 <option value="F81">F81</option>
121 <option value="F81+I">F81+I</option>
122 <option value="F81+G">F81+G</option>
123 <option value="F81+I+G">F81+I+G</option>
124 <option value="F81+R2">F81+R2</option>
125 <option value="F81+R3">F81+R3</option>
126 <option value="F81+R4">F81+R4</option>
127 <option value="F81+R5">F81+R5</option>
128 <option value="F81+R6">F81+R6</option>
129 <option value="F81+R7">F81+R7</option>
130 <option value="F81+R8">F81+R8</option>
131 <option value="F81+R9">F81+R9</option>
132 <option value="F81+R10">F81+R10</option>
133 <option value="K80">K80</option>
134 <option value="K80+I">K80+I</option>
135 <option value="K80+G">K80+G</option>
136 <option value="K80+I+G">K80+I+G</option>
137 <option value="K80+R2">K80+R2</option>
138 <option value="K80+R3">K80+R3</option>
139 <option value="K80+R4">K80+R4</option>
140 <option value="K80+R5">K80+R5</option>
141 <option value="K80+R6">K80+R6</option>
142 <option value="K80+R7">K80+R7</option>
143 <option value="K80+R8">K80+R8</option>
144 <option value="K80+R9">K80+R9</option>
145 <option value="K80+R10">K80+R10</option>
146 <option value="HKY">HKY</option>
147 <option value="HKY+I">HKY+I</option>
148 <option value="HKY+G">HKY+G</option>
149 <option value="HKY+I+G">HKY+I+G</option>
150 <option value="HKY+R2">HKY+R2</option>
151 <option value="HKY+R3">HKY+R3</option>
152 <option value="HKY+R4">HKY+R4</option>
153 <option value="HKY+R5">HKY+R5</option>
154 <option value="HKY+R6">HKY+R6</option>
155 <option value="HKY+R7">HKY+R7</option>
156 <option value="HKY+R8">HKY+R8</option>
157 <option value="HKY+R9">HKY+R9</option>
158 <option value="HKY+R10">HKY+R10</option>
159 <option value="TNe">TNe</option>
160 <option value="TNe+I">TNe+I</option>
161 <option value="TNe+G">TNe+G</option>
162 <option value="TNe+I+G">TNe+I+G</option>
163 <option value="TNe+R2">TNe+R2</option>
164 <option value="TNe+R3">TNe+R3</option>
165 <option value="TNe+R4">TNe+R4</option>
166 <option value="TNe+R5">TNe+R5</option>
167 <option value="TNe+R6">TNe+R6</option>
168 <option value="TNe+R7">TNe+R7</option>
169 <option value="TNe+R8">TNe+R8</option>
170 <option value="TNe+R9">TNe+R9</option>
171 <option value="TNe+R10">TNe+R10</option>
172 <option value="TN">TN</option>
173 <option value="TN+I">TN+I</option>
174 <option value="TN+G">TN+G</option>
175 <option value="TN+I+G">TN+I+G</option>
176 <option value="TN+R2">TN+R2</option>
177 <option value="TN+R3">TN+R3</option>
178 <option value="TN+R4">TN+R4</option>
179 <option value="TN+R5">TN+R5</option>
180 <option value="TN+R6">TN+R6</option>
181 <option value="TN+R7">TN+R7</option>
182 <option value="TN+R8">TN+R8</option>
183 <option value="TN+R9">TN+R9</option>
184 <option value="TN+R10">TN+R10</option>
185 <option value="K81">K81</option>
186 <option value="K81+I">K81+I</option>
187 <option value="K81+G">K81+G</option>
188 <option value="K81+I+G">K81+I+G</option>
189 <option value="K81+R2">K81+R2</option>
190 <option value="K81+R3">K81+R3</option>
191 <option value="K81+R4">K81+R4</option>
192 <option value="K81+R5">K81+R5</option>
193 <option value="K81+R6">K81+R6</option>
194 <option value="K81+R7">K81+R7</option>
195 <option value="K81+R8">K81+R8</option>
196 <option value="K81+R9">K81+R9</option>
197 <option value="K81+R10">K81+R10</option>
198 <option value="K81u">K81u</option>
199 <option value="K81u+I">K81u+I</option>
200 <option value="K81u+G">K81u+G</option>
201 <option value="K81u+I+G">K81u+I+G</option>
202 <option value="K81u+R2">K81u+R2</option>
203 <option value="K81u+R3">K81u+R3</option>
204 <option value="K81u+R4">K81u+R4</option>
205 <option value="K81u+R5">K81u+R5</option>
206 <option value="K81u+R6">K81u+R6</option>
207 <option value="K81u+R7">K81u+R7</option>
208 <option value="K81u+R8">K81u+R8</option>
209 <option value="K81u+R9">K81u+R9</option>
210 <option value="K81u+R10">K81u+R10</option>
211 <option value="TPM2">TPM2</option>
212 <option value="TPM2+I">TPM2+I</option>
213 <option value="TPM2+G">TPM2+G</option>
214 <option value="TPM2+I+G">TPM2+I+G</option>
215 <option value="TPM2+R2">TPM2+R2</option>
216 <option value="TPM2+R3">TPM2+R3</option>
217 <option value="TPM2+R4">TPM2+R4</option>
218 <option value="TPM2+R5">TPM2+R5</option>
219 <option value="TPM2+R6">TPM2+R6</option>
220 <option value="TPM2+R7">TPM2+R7</option>
221 <option value="TPM2+R8">TPM2+R8</option>
222 <option value="TPM2+R9">TPM2+R9</option>
223 <option value="TPM2+R10">TPM2+R10</option>
224 <option value="TPM2u">TPM2u</option>
225 <option value="TPM2u+I">TPM2u+I</option>
226 <option value="TPM2u+G">TPM2u+G</option>
227 <option value="TPM2u+I+G">TPM2u+I+G</option>
228 <option value="TPM2u+R2">TPM2u+R2</option>
229 <option value="TPM2u+R3">TPM2u+R3</option>
230 <option value="TPM2u+R4">TPM2u+R4</option>
231 <option value="TPM2u+R5">TPM2u+R5</option>
232 <option value="TPM2u+R6">TPM2u+R6</option>
233 <option value="TPM2u+R7">TPM2u+R7</option>
234 <option value="TPM2u+R8">TPM2u+R8</option>
235 <option value="TPM2u+R9">TPM2u+R9</option>
236 <option value="TPM2u+R10">TPM2u+R10</option>
237 <option value="TPM3">TPM3</option>
238 <option value="TPM3+I">TPM3+I</option>
239 <option value="TPM3+G">TPM3+G</option>
240 <option value="TPM3+I+G">TPM3+I+G</option>
241 <option value="TPM3+R2">TPM3+R2</option>
242 <option value="TPM3+R3">TPM3+R3</option>
243 <option value="TPM3+R4">TPM3+R4</option>
244 <option value="TPM3+R5">TPM3+R5</option>
245 <option value="TPM3+R6">TPM3+R6</option>
246 <option value="TPM3+R7">TPM3+R7</option>
247 <option value="TPM3+R8">TPM3+R8</option>
248 <option value="TPM3+R9">TPM3+R9</option>
249 <option value="TPM3+R10">TPM3+R10</option>
250 <option value="TPM3u">TPM3u</option>
251 <option value="TPM3u+I">TPM3u+I</option>
252 <option value="TPM3u+G">TPM3u+G</option>
253 <option value="TPM3u+I+G">TPM3u+I+G</option>
254 <option value="TPM3u+R2">TPM3u+R2</option>
255 <option value="TPM3u+R3">TPM3u+R3</option>
256 <option value="TPM3u+R4">TPM3u+R4</option>
257 <option value="TPM3u+R5">TPM3u+R5</option>
258 <option value="TPM3u+R6">TPM3u+R6</option>
259 <option value="TPM3u+R7">TPM3u+R7</option>
260 <option value="TPM3u+R8">TPM3u+R8</option>
261 <option value="TPM3u+R9">TPM3u+R9</option>
262 <option value="TPM3u+R10">TPM3u+R10</option>
263 <option value="TIMe">TIMe</option>
264 <option value="TIMe+I">TIMe+I</option>
265 <option value="TIMe+G">TIMe+G</option>
266 <option value="TIMe+I+G">TIMe+I+G</option>
267 <option value="TIMe+R2">TIMe+R2</option>
268 <option value="TIMe+R3">TIMe+R3</option>
269 <option value="TIMe+R4">TIMe+R4</option>
270 <option value="TIMe+R5">TIMe+R5</option>
271 <option value="TIMe+R6">TIMe+R6</option>
272 <option value="TIMe+R7">TIMe+R7</option>
273 <option value="TIMe+R8">TIMe+R8</option>
274 <option value="TIMe+R9">TIMe+R9</option>
275 <option value="TIMe+R10">TIMe+R10</option>
276 <option value="TIM">TIM</option>
277 <option value="TIM+I">TIM+I</option>
278 <option value="TIM+G">TIM+G</option>
279 <option value="TIM+I+G">TIM+I+G</option>
280 <option value="TIM+R2">TIM+R2</option>
281 <option value="TIM+R3">TIM+R3</option>
282 <option value="TIM+R4">TIM+R4</option>
283 <option value="TIM+R5">TIM+R5</option>
284 <option value="TIM+R6">TIM+R6</option>
285 <option value="TIM+R7">TIM+R7</option>
286 <option value="TIM+R8">TIM+R8</option>
287 <option value="TIM+R9">TIM+R9</option>
288 <option value="TIM+R10">TIM+R10</option>
289 <option value="TIM2e">TIM2e</option>
290 <option value="TIM2e+I">TIM2e+I</option>
291 <option value="TIM2e+G">TIM2e+G</option>
292 <option value="TIM2e+I+G">TIM2e+I+G</option>
293 <option value="TIM2e+R2">TIM2e+R2</option>
294 <option value="TIM2e+R3">TIM2e+R3</option>
295 <option value="TIM2e+R4">TIM2e+R4</option>
296 <option value="TIM2e+R5">TIM2e+R5</option>
297 <option value="TIM2e+R6">TIM2e+R6</option>
298 <option value="TIM2e+R7">TIM2e+R7</option>
299 <option value="TIM2e+R8">TIM2e+R8</option>
300 <option value="TIM2e+R9">TIM2e+R9</option>
301 <option value="TIM2e+R10">TIM2e+R10</option>
302 <option value="TIM2">TIM2</option>
303 <option value="TIM2+I">TIM2+I</option>
304 <option value="TIM2+G">TIM2+G</option>
305 <option value="TIM2+I+G">TIM2+I+G</option>
306 <option value="TIM2+R2">TIM2+R2</option>
307 <option value="TIM2+R3">TIM2+R3</option>
308 <option value="TIM2+R4">TIM2+R4</option>
309 <option value="TIM2+R5">TIM2+R5</option>
310 <option value="TIM2+R6">TIM2+R6</option>
311 <option value="TIM2+R7">TIM2+R7</option>
312 <option value="TIM2+R8">TIM2+R8</option>
313 <option value="TIM2+R9">TIM2+R9</option>
314 <option value="TIM2+R10">TIM2+R10</option>
315 <option value="TIM3e">TIM3e</option>
316 <option value="TIM3e+I">TIM3e+I</option>
317 <option value="TIM3e+G">TIM3e+G</option>
318 <option value="TIM3e+I+G">TIM3e+I+G</option>
319 <option value="TIM3e+R2">TIM3e+R2</option>
320 <option value="TIM3e+R3">TIM3e+R3</option>
321 <option value="TIM3e+R4">TIM3e+R4</option>
322 <option value="TIM3e+R5">TIM3e+R5</option>
323 <option value="TIM3e+R6">TIM3e+R6</option>
324 <option value="TIM3e+R7">TIM3e+R7</option>
325 <option value="TIM3e+R8">TIM3e+R8</option>
326 <option value="TIM3e+R9">TIM3e+R9</option>
327 <option value="TIM3e+R10">TIM3e+R10</option>
328 <option value="TIM3">TIM3</option>
329 <option value="TIM3+I">TIM3+I</option>
330 <option value="TIM3+G">TIM3+G</option>
331 <option value="TIM3+I+G">TIM3+I+G</option>
332 <option value="TIM3+R2">TIM3+R2</option>
333 <option value="TIM3+R3">TIM3+R3</option>
334 <option value="TIM3+R4">TIM3+R4</option>
335 <option value="TIM3+R5">TIM3+R5</option>
336 <option value="TIM3+R6">TIM3+R6</option>
337 <option value="TIM3+R7">TIM3+R7</option>
338 <option value="TIM3+R8">TIM3+R8</option>
339 <option value="TIM3+R9">TIM3+R9</option>
340 <option value="TIM3+R10">TIM3+R10</option>
341 <option value="TVMe">TVMe</option>
342 <option value="TVMe+I">TVMe+I</option>
343 <option value="TVMe+G">TVMe+G</option>
344 <option value="TVMe+I+G">TVMe+I+G</option>
345 <option value="TVMe+R2">TVMe+R2</option>
346 <option value="TVMe+R3">TVMe+R3</option>
347 <option value="TVMe+R4">TVMe+R4</option>
348 <option value="TVMe+R5">TVMe+R5</option>
349 <option value="TVMe+R6">TVMe+R6</option>
350 <option value="TVMe+R7">TVMe+R7</option>
351 <option value="TVMe+R8">TVMe+R8</option>
352 <option value="TVMe+R9">TVMe+R9</option>
353 <option value="TVMe+R10">TVMe+R10</option>
354 <option value="TVM">TVM</option>
355 <option value="TVM+I">TVM+I</option>
356 <option value="TVM+G">TVM+G</option>
357 <option value="TVM+I+G">TVM+I+G</option>
358 <option value="TVM+R2">TVM+R2</option>
359 <option value="TVM+R3">TVM+R3</option>
360 <option value="TVM+R4">TVM+R4</option>
361 <option value="TVM+R5">TVM+R5</option>
362 <option value="TVM+R6">TVM+R6</option>
363 <option value="TVM+R7">TVM+R7</option>
364 <option value="TVM+R8">TVM+R8</option>
365 <option value="TVM+R9">TVM+R9</option>
366 <option value="TVM+R10">TVM+R10</option>
367 <option value="SYM">SYM</option>
368 <option value="SYM+I">SYM+I</option>
369 <option value="SYM+G">SYM+G</option>
370 <option value="SYM+I+G">SYM+I+G</option>
371 <option value="SYM+R2">SYM+R2</option>
372 <option value="SYM+R3">SYM+R3</option>
373 <option value="SYM+R4">SYM+R4</option>
374 <option value="SYM+R5">SYM+R5</option>
375 <option value="SYM+R6">SYM+R6</option>
376 <option value="SYM+R7">SYM+R7</option>
377 <option value="SYM+R8">SYM+R8</option>
378 <option value="SYM+R9">SYM+R9</option>
379 <option value="SYM+R10">SYM+R10</option>
380 <option value="GTR">GTR</option>
381 <option value="GTR+I">GTR+I</option>
382 <option value="GTR+G">GTR+G</option>
383 <option value="GTR+I+G">GTR+I+G</option>
384 <option value="GTR+R2">GTR+R2</option>
385 <option value="GTR+R3">GTR+R3</option>
386 <option value="GTR+R4">GTR+R4</option>
387 <option value="GTR+R5">GTR+R5</option>
388 <option value="GTR+R6">GTR+R6</option>
389 <option value="GTR+R7">GTR+R7</option>
390 <option value="GTR+R8">GTR+R8</option>
391 <option value="GTR+R9">GTR+R9</option>
392 <option value="GTR+R10">GTR+R10</option>
393 <option value="MFP">MFP</option>
394 <option value="TEST">TEST</option>
395 </param>
396 <param label="--p-bootstrap-replicates: INTEGER Range(1000, None) The number of bootstrap searches to perform. Minimum of 1000 recomended. [default: 1000]" min="1000" name="pbootstrapreplicates" optional="True" type="integer" value="1000" />
397 <param label="--p-n-init-pars-trees: INTEGER Range(1, None) Number of initial parsimony trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pninitparstrees" optional="False" type="text" />
398 <param label="--p-n-top-init-trees: INTEGER Range(1, None) Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pntopinittrees" optional="False" type="text" />
399 <param label="--p-n-best-retain-trees: INTEGER Range(1, None) Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnbestretaintrees" optional="False" type="text" />
400 <param label="--p-stop-iter: INTEGER Number of unsuccessful iterations to stop. If not Range(1, None) set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pstopiter" optional="False" type="text" />
401 <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 1.0) Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pperturbnnistrength" optional="False" type="text" />
402 <param label="--p-spr-radius: INTEGER Radius for parsimony SPR search. If not set, Range(1, None) program defaults will be used. See IQ-TREE manual for details. [optional]" name="psprradius" optional="False" type="text" />
403 <param label="--p-n-max-ufboot-iter: INTEGER Range(1, None) Maximum number of iterations. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pnmaxufbootiter" optional="False" type="text" />
404 <param label="--p-n-ufboot-steps: INTEGER Range(1, None) Number of iterations for UFBoot stopping rule. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pnufbootsteps" optional="False" type="text" />
405 <param label="--p-min-cor-ufboot: NUMBER Range(0.51, 0.99) Minimum correlation coefficient. If not set, program defaults will be used.See IQ-TREE manual for details. [optional]" name="pmincorufboot" optional="False" type="text" />
406 <param label="--p-ep-break-ufboot: NUMBER Range(0.01, 0.99) Epsilon value to break tie. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pepbreakufboot" optional="False" type="text" />
407 <param label="--p-allnni: --p-allnni: / --p-no-allnni Perform more thorough NNI search. [default: False]" name="pallnni" selected="False" type="boolean" />
408 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes. [optional]" name="palrt" optional="False" type="text" />
409 <param label="--p-abayes: --p-abayes: / --p-no-abayes Single branch test method. Performs an approximate Bayes test. Can be used with other \'single branch test methods\' and ultrafast bootstrap. Values reported in the order of: alrt, lbp, abayes, ufboot. [default: False]" name="pabayes" selected="False" type="boolean" />
410 <param label="--p-lbp: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other \'single branch test methods\'. Values reported in the order of: alrt, lbp, abayes, ufboot. [optional]" name="plbp" optional="False" type="text" />
411 <param label="--p-bnni: --p-bnni: / --p-no-bnni Optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations. [default: False]" name="pbnni" selected="False" type="boolean" />
412 <param label="--p-safe: --p-safe: / --p-no-safe Safe likelihood kernel to avoid numerical underflow. [default: False]" name="psafe" selected="False" type="boolean" />
413 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
414
415 </inputs>
416
417 <outputs>
418 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
419
420 </outputs>
421
422 <help><![CDATA[
423 Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
424 ###############################################################
425
426 Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
427 automatic model selection and bootstrap supports.
428
429 Parameters
430 ----------
431 alignment : FeatureData[AlignedSequence]
432 Aligned sequences to be used for phylogenetic reconstruction.
433 seed : Int, optional
434 Random number seed. If not set, program defaults will be used. See IQ-
435 TREE manual for details.
436 n_cores : Int % Range(1, None) | Str % Choices('auto'), optional
437 The number of cores to use for parallel processing. Use `auto` to let
438 IQ-TREE automatically determine the optimal number of cores to use.
439 n_cores_max : Int % Range(2, None), optional
440 Limits the maximum number of cores to be used when 'n_cores' is set to
441 'auto'.
442 n_runs : Int % Range(1, None), optional
443 Number of indepedent runs. Multiple independent runs (e.g. 10) can
444 outperform a single run in terms of likelihood maximisation.
445 substitution_model : Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional
446 Model of Nucleotide Substitution.If not provided, IQ-TREE will
447 determine the best fit substitution model automatically.
448 bootstrap_replicates : Int % Range(1000, None), optional
449 The number of bootstrap searches to perform. Minimum of 1000
450 recomended.
451 n_init_pars_trees : Int % Range(1, None), optional
452 Number of initial parsimony trees. If not set, program defaults will be
453 used. See IQ-TREE manual for details.
454 n_top_init_trees : Int % Range(1, None), optional
455 Number of top initial trees. If not set, program defaults will be used.
456 See IQ-TREE manual for details.
457 n_best_retain_trees : Int % Range(1, None), optional
458 Number of best trees retained during search. If not set, program
459 defaults will be used. See IQ-TREE manual for details.
460 stop_iter : Int % Range(1, None), optional
461 Number of unsuccessful iterations to stop. If not set, program defaults
462 will be used. See IQ-TREE manual for details.
463 perturb_nni_strength : Float % Range(0.01, 1.0), optional
464 Perturbation strength for randomized NNI. If not set, program defaults
465 will be used. See IQ-TREE manual for details.
466 spr_radius : Int % Range(1, None), optional
467 Radius for parsimony SPR search. If not set, program defaults will be
468 used. See IQ-TREE manual for details.
469 n_max_ufboot_iter : Int % Range(1, None), optional
470 Maximum number of iterations. If not set, program defaults will be
471 used. See IQ-TREE manual for details.
472 n_ufboot_steps : Int % Range(1, None), optional
473 Number of iterations for UFBoot stopping rule. If not set, program
474 defaults will be used.See IQ-TREE manual for details.
475 min_cor_ufboot : Float % Range(0.51, 0.99), optional
476 Minimum correlation coefficient. If not set, program defaults will be
477 used.See IQ-TREE manual for details.
478 ep_break_ufboot : Float % Range(0.01, 0.99), optional
479 Epsilon value to break tie. If not set, program defaults will be used.
480 See IQ-TREE manual for details.
481 allnni : Bool, optional
482 Perform more thorough NNI search.
483 alrt : Int % Range(1000, None), optional
484 Single branch test method. Number of bootstrap replicates to perform an
485 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
486 replicates is recomended. Can be used with other 'single branch test
487 methods'. Values reported in the order of: alrt, lbp, abayes.
488 abayes : Bool, optional
489 Single branch test method. Performs an approximate Bayes test. Can be
490 used with other 'single branch test methods' and ultrafast bootstrap.
491 Values reported in the order of: alrt, lbp, abayes, ufboot.
492 lbp : Int % Range(1000, None), optional
493 Single branch test method. Number of bootstrap replicates to perform a
494 fast local bootstrap probability method. Minimum of 1000 replicates is
495 recomended. Can be used with other 'single branch test methods'. Values
496 reported in the order of: alrt, lbp, abayes, ufboot.
497 bnni : Bool, optional
498 Optimize UFBoot trees by NNI on bootstrap alignment. This option
499 reduces the risk of overestimating branch supports with UFBoot due to
500 severe model violations.
501 safe : Bool, optional
502 Safe likelihood kernel to avoid numerical underflow.
503
504 Returns
505 -------
506 tree : Phylogeny[Unrooted]
507 The resulting phylogenetic tree.
508 ]]></help>
509 <macros>
510 <import>qiime_citation.xml</import>
511 </macros>
512 <expand macro="qiime_citation"/>
513 </tool>